Journal: Biotechnology Reports

Article Title: Integrative analysis of RAS signaling effectors reveals stage-dependent oncogenic patterns in colon adenocarcinoma

doi: 10.1016/j.btre.2025.e00902

Figure Lengend Snippet: Validation of the core RAS effector expression changes in COAD patient’s samples. The left panel (A) illustrates gene expression changes across stages using TCGA data, while the right panel (B) presents results from analysis of a tissue cDNA array via qPCR. (C) The available protein expression levels of core RAS effectors were examined using data from the UALCAN proteomics database.

Article Snippet: We used TissueScan Colorectal Cancer cDNA arrays (OriGene Technologies Inc., Rockville, MD, USA, Cat#: HCRT502, LOT:TH25) to measure the expression levels of key RAS effectors.

Techniques: Biomarker Discovery, Expressing, Gene Expression

Journal: Biotechnology Reports

Article Title: Integrative analysis of RAS signaling effectors reveals stage-dependent oncogenic patterns in colon adenocarcinoma

doi: 10.1016/j.btre.2025.e00902

Figure Lengend Snippet: Correlation analysis of the core RAS effectors based on qPCR results of COAD patient’s samples. Pearson’s correlation coefficients were calculated for the five selected RAS effectors to analyze co-expression patterns in normal (A), COAD tumor (B), and Stage I COAD (C) samples. Heatmaps were created using tissue cDNA array results. The correlation coefficients, ranging from −1 to 1, represent the strength and direction of the relationships. The size of the circles reflects the magnitude of the correlation, with red indicating positive correlation and blue representing negative correlation between gene pairs. (D-E) The early tumorigenic impact of core RAS effector gene expression dynamics at the normal-to-cancer transition.

Article Snippet: We used TissueScan Colorectal Cancer cDNA arrays (OriGene Technologies Inc., Rockville, MD, USA, Cat#: HCRT502, LOT:TH25) to measure the expression levels of key RAS effectors.

Techniques: Expressing, Gene Expression

Journal: Biotechnology Reports

Article Title: Integrative analysis of RAS signaling effectors reveals stage-dependent oncogenic patterns in colon adenocarcinoma

doi: 10.1016/j.btre.2025.e00902

Figure Lengend Snippet: (A) Linear discriminant analysis (LDA) was performed on the tissue cDNA array dataset, combining the expression levels of five core RAS effectors, then determined the separation efficiency between normal samples and the samples representing the four stages of COAD. (B) The LD1 axis projection of the LDA analysis. Confusion matrices were generated by integrating the expression profiles of the five core RAS effectors, applied to the TCGA dataset (C) and tissue cDNA array dataset (D).

Article Snippet: We used TissueScan Colorectal Cancer cDNA arrays (OriGene Technologies Inc., Rockville, MD, USA, Cat#: HCRT502, LOT:TH25) to measure the expression levels of key RAS effectors.

Techniques: Expressing, Generated

Journal: Biotechnology Reports

Article Title: Integrative analysis of RAS signaling effectors reveals stage-dependent oncogenic patterns in colon adenocarcinoma

doi: 10.1016/j.btre.2025.e00902

Figure Lengend Snippet: Validation of the core RAS effector expression changes in COAD patient’s samples. The left panel (A) illustrates gene expression changes across stages using TCGA data, while the right panel (B) presents results from analysis of a tissue cDNA array via qPCR. (C) The available protein expression levels of core RAS effectors were examined using data from the UALCAN proteomics database.

Article Snippet: OriGene Tissue cDNA Arrays, such as the TissueScanTM Cancer and Normal Tissue cDNA Arrays, are commercially available kits for gene expression analysis using human tissue samples.

Techniques: Biomarker Discovery, Expressing, Gene Expression

Journal: Biotechnology Reports

Article Title: Integrative analysis of RAS signaling effectors reveals stage-dependent oncogenic patterns in colon adenocarcinoma

doi: 10.1016/j.btre.2025.e00902

Figure Lengend Snippet: Correlation analysis of the core RAS effectors based on qPCR results of COAD patient’s samples. Pearson’s correlation coefficients were calculated for the five selected RAS effectors to analyze co-expression patterns in normal (A), COAD tumor (B), and Stage I COAD (C) samples. Heatmaps were created using tissue cDNA array results. The correlation coefficients, ranging from −1 to 1, represent the strength and direction of the relationships. The size of the circles reflects the magnitude of the correlation, with red indicating positive correlation and blue representing negative correlation between gene pairs. (D-E) The early tumorigenic impact of core RAS effector gene expression dynamics at the normal-to-cancer transition.

Article Snippet: OriGene Tissue cDNA Arrays, such as the TissueScanTM Cancer and Normal Tissue cDNA Arrays, are commercially available kits for gene expression analysis using human tissue samples.

Techniques: Expressing, Gene Expression

Journal: Biotechnology Reports

Article Title: Integrative analysis of RAS signaling effectors reveals stage-dependent oncogenic patterns in colon adenocarcinoma

doi: 10.1016/j.btre.2025.e00902

Figure Lengend Snippet: (A) Linear discriminant analysis (LDA) was performed on the tissue cDNA array dataset, combining the expression levels of five core RAS effectors, then determined the separation efficiency between normal samples and the samples representing the four stages of COAD. (B) The LD1 axis projection of the LDA analysis. Confusion matrices were generated by integrating the expression profiles of the five core RAS effectors, applied to the TCGA dataset (C) and tissue cDNA array dataset (D).

Article Snippet: OriGene Tissue cDNA Arrays, such as the TissueScanTM Cancer and Normal Tissue cDNA Arrays, are commercially available kits for gene expression analysis using human tissue samples.

Techniques: Expressing, Generated

Journal: The Journal of Cell Biology

Article Title: Epigenetic deprogramming by disruption of CIZ1-RNA nuclear assemblies in early-stage breast cancers

doi: 10.1083/jcb.202409123

Figure Lengend Snippet: (Related to and ). CIZ1 domains, transcript levels , and domain expression in common solid tumors. (A) Protein domain map aligning human ( NP_001124488.1 ) and mouse ( NP_082688.1 ) CIZ1. Numbers correspond to amino acids encoded at exon boundaries. The domains highlighted are: Prion-like domains 1 and 2 (PLD1 and PLD2, purple) at positions 1–78 and 360–451, respectively (human), and positions 1–67 and 361–399, respectively (mouse), 10 three zinc fingers (ZnF_C2H2 SM00355, ZF_C2H2 sd00020, and ZF_C2H2 sd00020, blue) at positions 593–617, 656–676, and 687–709, respectively (human), and 537–561, 600–620, and 631–653, respectively (mouse), an acidic domain (red) containing a concentrated area of aspartates and glutamates at position 741–761 (human) and 689–709 (mouse), and a matrin-3 homology domain (ZnF_U1 smart0045, yellow) at position 796–831 (human) and 746–770 (mouse). Box shows % identity at the amino acid level across these domains. Human and mouse CIZ1 are 65% identical at the protein level, with identity concentrated in the conserved domains (up to 96%). (B) Bright-field images of breast-derived cell types ordered based on phenotype, with corresponding hormone and growth factor receptor status. The bar is 100 μm. (C) CIZ1 locus in Homo sapiens with corresponding exon numbers. Potential CIZ1 alternative transcription start sites (TSSs) in exons 10 and 11 predicted in the FANTOM5 project are indicated (red stars). The coding sequence would be expected to begin at a methionine in exon 11. The chromatin landscape in human mammary epithelial cells (HMEC), a cervical cancer cell line (HeLa) and a breast cancer cell line (MCF7) is shown below. Diagram generated using UCSC genome browser . (D) Total CIZ1 TPM derived from the indicated number of cancer (C) and normal (N) tissues in TCGA compared using GEPIA for the indicated disease types. No significant difference is detected (where log 2 FC was >1, and P value <0.05) when comparing all amalgamated transcripts that map to the CIZ1 gene (unresolved by exon). (E) Relative expression of exons 7 (red) and 16 (blue), normalized to the average of three unmatched control samples for each of six common solid tumor types in multi-tissue cDNA array CSRT101. Individual patient data plus the average of the controls calibrated to 1 (Av.C, left) and data aggregated by disease stage (0–IV, right) are shown. 0 represents histologically normal tissue. Individual sample information for all arrays is given in .

Article Snippet: TissueScan cancer and normal tissue cDNA arrays , Origene , https://www.origene.com/products/tissues/tissuescan.

Techniques: Expressing, Zinc-Fingers, Derivative Assay, Sequencing, Generated, Control

Journal: The Journal of Cell Biology

Article Title: Epigenetic deprogramming by disruption of CIZ1-RNA nuclear assemblies in early-stage breast cancers

doi: 10.1083/jcb.202409123

Figure Lengend Snippet: Resources

Article Snippet: TissueScan cancer and normal tissue cDNA arrays , Origene , https://www.origene.com/products/tissues/tissuescan.

Techniques: Virus, Recombinant, Transfection, Protease Inhibitor, Mutagenesis, Plasmid Preparation, Generated, Sequencing, Software, Gene Expression, Functional Assay, Inverted Microscopy